Coming out of Darkness
by DJFireHawk
Summary: During the events with Khan and Admiral Marcus Kirk forges a friendship with Khan. When Uhura yells at Spock that Khan may be the only way to save him he surrenders, in return Jim speaks on his behalf at his trial and Khan is released…with a few conditions. Starts on Cronos.
1. Chapter 1

Coming out of Darkness

Summary: During the events with Khan and Admiral Marcus Kirk forges a friendship with Khan. When Uhura yells at Spock that Khan may be the only way to save him he surrenders, in return Jim speaks on his behalf at his trial and Khan is released…with a few conditions. Starts on Cronos.

Warnings: Spoilers for Into Darkness. Slash, M/M, etc…if you've read any of my other fics this should not be a shock ^.^ Also…I sadly own nothing but my idea…I'm just borrowing the wonderful characters.

A/N: I saw the movie and my mind immediately brought out this idea which refused to rest…so here it is. I'm uploading the whole thing at once too.

Chapter 1

Cronos, the Klingon's home planet and the worst possible place for any member of Starfleet to end up. So why was Jim there watching Uhura being lifted off the ground by her throat? He growled softly, ready to run to her aid when a beam of light took out the Klingon holding her. Chaos promptly ensued as he and Spock lead the security officers out into the fight. He cursed violently when the two security men fell to the Klingons, but he had little time for concern as a group of the violent bastards was on him. One was about to crush his skull when another flash of light had the Klingons on the ground. He barely locked onto a pair of impossibly dark eyes before Uhura and Spock were dragging him behind some stone rubble for protection. Jim watched as the man they were after finished taking out an entire squadron of Klingons by himself.

"What the hell did they feed that guy?"

Uhura's half amused and half exasperated look made him grin slightly before their quarry stepped closer, blasting Spock's phaser rifle out of his hand like it was a toy. Jim wasn't sure of the man's motives but he was fairly certain if he had wanted them dead he wouldn't have saved them from the Klingons in the first place. The man asked how many missiles they had, and when Spock told him he simply surrendered. Jim stood to look him in the eye and accept his surrender, before punching him in the face repeatedly until he could no longer lift his arms.

"Captain!"

Uhura's cry caused a spark of something to appear in the man's eyes as he whispered the same word, sending an involuntary shiver through Jim before he told Spock to cuff him. Once they had him aboard the ship and safely contained in a cell in the brig Jim had Bones take a blood sample to find out what the hell made him so powerful. Harrison was surprisingly cooperative, and entirely too perceptive when he figured out that they weren't moving because of a warp core malfunction. When the man spoke as he and Spock were leaving he ignored Spock's warning, sending him back to the bridge, and returned to speak to his prisoner again.

"I watched you murder innocent men and women! I was authorized to end you…and the only reason you are still alive is because I am allowing it. So shut your mouth."

Harrison regarded the Captain silently for a moment before speaking, his rich baritone voice seeming to fill the space around them.

"I surrendered to you because, despite your attempts to convince me otherwise, you seem to have a conscience. I would have no chance to convince you of the truth otherwise. 2-3, 1-7, 4-6, 1-1. Coordinates not far from Earth. If you wish to know why I did what I did, go and take a look."

"Give me one reason why I should listen to you."

The Captain was glaring harshly at him and, as he tried to figure out why, something he had said back on Cronos clicked into place and he knew.

"I can give you 72...and they're here on your ship. I suggest you open one up."

Harrison paused a moment to let that sink in before speaking in a softer tone.

"Tell me something Captain…You mentioned a name when you accepted my surrender…a man named Pike. Who was he to you?"

He watched the younger man's glare soften with sorrow before he looked away.

"He was my mentor, my friend, and one of the best damned men I have ever known in my life."

As Jim turned to walk away he nearly missed the soft look of guilt that settled on Harrison's face…nearly.

He called Scotty, hoping that he'd check out the coordinates despite having resigned b/c Jim was an idiot…again.

Upon reaching the bridge he informed Bones and Spock of his plan to open one of the torpedoes.

"Are you outta your corn-fed mind? You're not actually gonna listen to this guy? He killed Pike, he almost killed you. Now you think it's a good idea to pop open a torpedo because he dared you to."

"Why did he save our lives Bones?"

"The Doctor does have a point Captain."

"Don't agree with me Spock, it makes me very uncomfortable."

Jim listened to Bones and Spock go back and forth a bit before intervening.

"Look we're gonna open up a torpedo the question is how."

"But Jim, without Mr. Scott onboard who exactly is qualified to just pop open a four ton stick of dynamite?"

Jim grinned and almost let out a laugh before Spock spoke up.

"The Admiral's daughter appeared to have interest in the torpedoes and she is a weapons specialist. Perhaps she could be of some use."

Jim turned to give his First Officer a confused look.

"What Admiral's daughter?"

"Carol Marcus. Your new science officer concealed her identity to board the ship."

Jim's face took on an amused yet slightly confused look at the same time.

"When were you gonna tell me that?"

"When it became relevant…as it just did."

Jim let out an exasperated sound before comming the aforementioned woman and asking her to meet with him. After speaking with her he decided to send Bones with her to take a shuttle to a nearby planetoid to open up a missile.

"You know, when I dreamed about being stuck on a deserted planet with a gorgeous woman there was no torpedo."

"Dr. McCoy may I remind you, you are not there to flirt."

"So how can these legendary hands help you Dr. Marcus?"

"Bones."

Clearly Jim's warning was ignored as Bones tried to impress the woman with a story about delivering Gorn Octuplets. Jim and Sulu shared an amused look before Jim nearly had a heart attack from the missile arming itself, Carol barely managing to stop it in time. What he saw when they brought it back sent his mind reeling and had him racing back to the brig, Spock right on his heels. He stood close to the glass and refused to flinch or step back when Harrison pressed himself closer to the glass between them.

"Something I can help you with…Captain?"

Jim suppressed a shiver and stared blankly at the man as he tried to suppress his confusion and curiosity.

"Why is there a man in that torpedo?"

"There are men and women in all those torpedoes Captain…I put them there."

"Who the hell are you?"

Harrison gave Jim a an odd look before answering slowly.

"A remnant of a time long past…genetically engineered to be superior so as to lead others to peace in a world at war. We were condemned as criminals and forced into exile. For centuries we slept, hoping that when we awoke things would be different…better. As a result of the destruction of Vulcan your Starfleet began to aggressively search distant quadrants of space. My ship was found adrift, I alone was revived."

"I looked up John Harrison. Until a year ago he didn't exist."

"John Harrison was a fiction, created the moment I was awoken by your Admiral Marcus to help him advance his cause. A smoke-screen to conceal my true identity. My name…is Khan."

The look Harrison gave him was one Jim was unsure how to interpret, could only name as intense.

"Why would a Starfleet Admiral ask a 300 year old frozen man for help?"

Khan gave Jim an amused smirk at his sarcasm, liking the bold young Captain more and more.

"Because I am better."

"At what?"

"Everything."

Jim felt Khan's low voice, felt the hidden danger and power in it, flowing over his senses like silk. Khan could see the reactions Jim was trying to hide from him and it only made him more interested in the younger male.

"Alexander Marcus needed to respond to an uncivilized threat in a civilized time, and for that he needed a warrior's mind…my mind…to design weapons and warships."

"You are suggesting that Admiral Marcus violated the very regulations he vowed to uphold simply because he wanted to exploit your intellect?"

Jim sighed softly and let his forehead thunk softly against the glass, trying to decide if Spock would hit him for laughing at his naivety about human behavior. Khan spared Jim a momentary glance filled with understanding before hissing at Spock in a dangerous tone.

"He wanted to exploit my savagery. Intellect alone is useless in a fight Mr. Spock. You can't even break a rule, how would you be expected to break bone?"

Khan noticed Jim's flinch at his words and resolved to find out later why he seemed to have a problem with that part of his little speech over any other.

"Marcus used me to design weapons to help him realize his vision of a militarized Starfleet. He sent you to use those weapons…to fire my torpedoes at an unsuspecting planet…and then he purposely crippled your ship in enemy space leading to one inevitable outcome. The Klingons would come looking for whomever was responsible, and you would have no chance of escape. Marcus would finally have the war he always talked about, the war he always wanted."

"No."

The harsh whisper from Jim made Khan frown at him.

"No. I watched you open fire on a room of unarmed Starfleet officers. You killed them in cold blood."

"Marcus took my crew from me."

Khan turned away from the other two men so they would not see the guilt and regret on his face at seeing the pain his attack had caused Jim…though he still heard it in the man's harsh and broken voice yelling at him.

"You are a murderer!"

"He used my friends to control me! I tried to smuggle them to safety by concealing them in the very weapons I had designed…but I was discovered. I had no choice but to escape alone. When I did I had every reason to suspect that Marcus had killed every single one of the people I hold most dear. So I responded in kind."

Khan turned to face them as a single tear made its way down his cheek and his voice softened. He watched Jim's harshness soften as understanding swept through him.

"My crew is my family. Is there anything you would not do for your family?"

Jim sighed softly. He could understand the man's reasons, he could, but he wasn't sure he could ever really forgive him for the loss of his mentor. He was about to speak only to be interrupted by Sulu comming him.

"Sir, proximity alert. There's a ship at warp heading right for us."

"Klingons?"

Khan shook his head at Jim for his question.

"At warp? No Jim. We both know who it is."

Sulu's reply confirmed that it wasn't coming from Cronos and Jim cursed fluently in several languages, making Khan and Spock both raise an eyebrow as they glanced at each other.


	2. Chapter 2

After hearing Sulu's words Jim missed the look shared by Spock and Khan as he turned to the security officer in the room.

"Cuff him and take him to Med-bay…I want a six man security detail on him at all times."

"Yes Captain."

Orders given to security Jim and Spock ran to the bridge. As Jim slid into his chair Uhura informed him they were being hailed so he told her to put it on screen and then told Sulu to broadcast it ship-wide for the record. The resulting conversation with Marcus, him firing on Jim's ship, them warping away only to be caught and fired right out of warp, Marcus beaming Carol onto the Vengeance, and then attempting to fire again only to be unable thanks to Scotty's interference…all of this made for one pissed off Captain who yet again ignored Spock's warnings and sent him back to the bridge so he could see Khan alone.

"Tell me everything you know about that damned ship."

"Dreadnaught class. Two times the size three times the speed. Advanced weaponry. Modified for a minimal crew. Unlike most Federation vessels it's built solely for combat."

"I will do everything I can to make you answer for what you did…but right now I need your help."

"In exchange for what?"

Jim sighed softly and looked Khan in the eyes.

"I was going to offer safety for your crew, but I can't guarantee my own crew's safety right now. The only thing I can offer you is a favor…anything you want within reason…and not against any of the vows I have taken…to be redeemed whenever you want it."

Jim watched something flash in Khan's eyes as he seemed to debate the offer in his head. Khan's mind whirled with the possibilities of all the things he could use Kirk's offer for.

"You coming with me or not?"

Minutes later found both of them both suited up and standing in a chamber as Jim spoke to Scotty via comm., preparing to be launched through space and through a door on the other ship. Scotty's reaction to finding the access port they needed to enter was rather amusing, even to Khan though Kirk's response amused him far more.

"Whoa whoa whoa hold on there Captain. This door is very wee, I mean ya know small. It's four square meters tops. It's gonna be like jumping out of a moving car, off a bridge, into your shot glass."

"It's ok I've done it before."

The look Khan gave him made Jim try to explain it only to give up when it just sounded ridiculous. They launched into space, dodging debris as they went. A piece hit Jim's visor making him lose his visor, forcing him to fly blind. Khan told him to pull back a bit and follow his lead, both of them safely arriving in the larger ship. After introducing Khan to Scotty the former began leading them through the ship towards the bridge. Once there Jim approached Marcus while Scotty stunned Khan. Scotty gave Jim an apologetic look.

"Sorry lad but Mr. Spock said he canna be trusted."

"He saved our lives Scotty…more than once now. I trust him…to a point."

Scotty looked guilty while Jim tried to get the Admiral to surrender. Khan had heard everything, including Jim's defense of him. That did not stop him from attacking Scotty, rendering him unconscious, and proceeding to knock Jim out as well. He shoved Marcus' daughter out of the way, breaking her leg in the process before crushing the Admiral's skull…though he did feel a bit guilty for his daughter having to see it. Khan turned to Jim who was trying to get back up and lifted him by his throat, pinning him to the wall.

"Captain…Jim…Why do you limit yourself with Starfleet? You are better than them…smarter and bolder. You could be so much more…"

"Starfleet does good…we help keep peace…Marcus does not represent all of us Khan…we're not all like him. I'M not like him."

"I know you aren't James. I need you to help me now. I want my crew back."

Khan hailed the Enterprise and picked up Kirk, showing him to Spock as he demanded his own crew be returned to him before throwing Jim back onto the floor. Spock seemed surprisingly willing to agree to the terms in Jim's opinion, even though he was laying on the ground struggling to get back up. Khan reached down to run a hand through Jim's hair as he moved to the control console.

"I see your 72 torpedoes are still in their tubes. If they are not mine Commander I will know it."

"Vulcan's do not lie…thee torpedoes are yours."

Khan transported the torpedoes onto his ship and sounded relieved when he spoke again.

"Thank you Mr. Spock."

"I have fulfilled your terms, now fulfill mine."

Khan beamed Jim, Scotty, and Carol back onto the ship…unfortunately directly into his former cell in the brig. When Jim finally reached the med-bay so Carol could get help he found out Spock had detonated the torpedoes. Khan's scream of rage was unknowingly echoed by an equally unhappy yell from Jim.

"What the hell did he just do Bones?! There were people in those things!"

"Spock's cold, but he's not that cold. I've got Khan's crew. 72 human popsicles safe and sound in their cryo tubes."

"Son of a bitch."

Jim sounded a bit awed at their audacity…particularly coming from Spock. A sudden loss of power made Jim curse even more as he and Scotty ran for engineering. The enterprise was heavily damaged from the Admiral's firing upon her and was going down with no power to stop her. The vengeance was having trouble staying out of Earth's gravitational pull as it too was now badly damaged. Khan was enraged by what he was as Spock's murder of his people. He pointed the ship towards Starfleet headquarters and let it fall.

At some point Scotty realized that the housings in the warp core were misaligned. Jim knocked him out and strapped him into a chair, venturing inside the warp core chamber alone, knowing the radiation would kill him. He made it, aligned the housings, and managed to make it back to the sealed chamber door…by sheer stubborn willpower. He managed to close the door and saw Spock kneeling outside the door. Jim's voice was weak but he had to know.

"How's our ship?"

"Out of danger. You saved the crew."

"You used what he wanted against him. That's a nice move. Making him think you killed his crew…not so much."

"It is what you would have done."

"And this…this is what you would have done. It was only logical. I'm scared Spock. Help me not be. How do you choose not to feel?"

"I do not know. Right now I am failing."

Jim heard the emotion in Spock's voice and felt somewhat soothed, knowing that he would be missed…be remembered.

"I want you to know why I couldn't let you die. Why I went back for you."

"Because you are my friend."

Seeing the Vulcan shed tears over him dying made something inside of Jim want to cry with him, though he had no energy to do so. He managed to put on hand on the glass, an action mirrored by Spock, and Jim moved his fingers to replicate Spock's gesture. He finally lost the battle between the radiation poisoning and his stubborn willpower, his hand sliding down the glass as Spock broke down and screamed in rage.

On Earth the vengeance crashed into Earth, narrowly missing the Enterprise on the way. Khan managed to get out and started running, especially after Spock beamed down and began chasing him. Bones had Jim in the med-bay and sat heavily in his chair…he'd just lost his best friend. A sudden sound from the table next to him made him shoot up as the dead Tribble he'd injected with Khan's blood came back to life. He commed Uhura on the bridge and told her to get Khan's ass back on the ship because his blood could save Jim's life. She beamed down onto where Spock and Khan were fighting and shot stunners at Khan. Khan and Spock fought some more until Uhura screamed for Spock to stop.

"Spock stop! We need him alive! He might be our only chance to save Kirk!"

Khan used Spock's moment of shock to incapacitate him and rounded on Uhura.

"What do you mean save him? What happened?"

"He…the warp core housings weren't aligned…he went inside…"

"Radiation poisoning…foolish, reckless, bold…Let's go…NOW!"

Uhura had them beamed back to the ship and Khan immediately ran into the med-bay, Uhura and a couple nurses moving Spock on a bio-bed behind him, and instructed Bones as to how to synthesize a serum from his blood to fix the Captain.

"It will take both serum and a direct transfusion of blood in order to fix the damage that was done…and even then he will need rest for sometime after."

While the transfusions took place Khan watched Jim for any sign of healing, any sign of life…and breathed a deep sigh as the other's chest began to rise and fall. The crew around them weeping in relief that their beloved Captain was alright made Khan realize just how great a man James Kirk really was. It made him that much more determined to keep him safe no matter the cost.


	3. Chapter 3

2 weeks later Jim woke up in a hospital bed to find Bones hovering over him with a scanner and groaned loudly.

"Oh don't be so melodramatic…you were barely dead. It's the transfusions that really took a toll. You were out cold for two weeks."

"Transfusions?"

"Your cells were heavily irradiated we had no choice."

"Khan."

"Once we got him back on board I synthesized a serum from his super blood. His instructions were precise and I had no choice but to trust him. We also had to do a direct transfusion of blood. Tell me…are you feeling homicidal, power mad, despotic?"

"No more than usual. How did you catch him?"

"I didn't."

Bones moved and Spock stepped forward.

"When Lieutenant Uhura beamed down and informed me that we needed Khan to save you…he incapacitated me in my momentary shock. Lieutenant Uhura informed me that he asked her what happened and when she told him he ordered her to take him to you. Once aboard the ship he headed directly to the med-bay and instructed Doctor McCoy how to synthesize the serum to bring you back."

Jim gave Spock a thoughtful look before speaking again.

"His trial?"

"Has been postponed until you are able to testify. The Admiral's council insisted upon it."

"Good…I want to testify…on his behalf."

"Captain?"

"Jim what the hell?"

Later Jim sat before the Admiral's council, and a room filled with cameras as he told them exactly what he had told his friends.

John Harrison, formerly known as Khan, acted out of justified fear for his own safety and that of his former crew. Admiral Marcus' actions towards him gave him no reason to believe anyone else in Starfleet would be different. When he met myself and my crew his opinions began to change. He saved our lives, twice, and saved my own twice as well. If not for his help Admiral Marcus would have succeeded in starting a war with the Klingon's, a war we do not need nor want. The crashing of the Vengeance into Earth was merely an accident caused by the malfunction of the ship, The Enterprise herself nearly had the same fate. I ask you to please consider a light sentence for him considering what he went through at the hands of Admiral Marcus."

The Admiral's council deliberated quietly amongst themselves while Khan gave Jim a surprised look from his place in the center of the room.

"We agree with you Captain Kirk. We will allow Mr. Harrison to be released so long as certain conditions are met. Firstly we will not be waking any of his fellow crew members until he himself can prove he is not a threat. Secondly, Captain Kirk, you and a select few you choose will take him to New Vulcan to be treated by their mind healers. Thirdly, once that is completed he will join with the crew of the Enterprise when she heads out on a 5 year mission. And lastly, if he takes any further actions against Starfleet…trying to destroy or take over in any way…he will be put back to sleep for good. Kirk…he will be your shadow aboard the Enterprise, and will do anything you require. These are the terms…Is that clear to both of you?"

Both men gave the affirmative and Khan was released to Jim's supervision. Jim stood, still shakey as he hadn't completely finished healing, and nearly fell over. He would have met the tiled floor if Khan hadn't caught him and commed Bones.

"Dr. McCoy…I have been released to Jim's supervision…I am sure he will give you all details later but right now he is nearly falling over…he has not finished healing yet."

Khan listened to the rather inventive string of curses from the doctor before he and Jim were both beamed back into the hospital room, much to Jim's rather vocal displeasure. Bones attempted to order Khan out of the room but he and Jim both protested the idea.

"He can't leave my side Bones…it's a condition of his release."

Bones let off a few more creative curses before finishing his scans and leaving the room. Khan sat on the edge of the bed next to Jim and gave him a fond look.

"James…do you realize what has happened to you?"

"Yeah…you helped Bones save my life…again."

"Not only that. By infusing you with my blood a bond was created. You and I are linked to each other Jim. If you are in pain I will know. If you are in danger I will know. I can feel what you feel and you can feel what I feel. Even Vulcan mind healers cannot erase it because it is in our blood.."

Khan managed to actually laugh for the first time in a long time when Jim cursed in multiple languages. He knew Jim wasn't truly angry about it…he could feel something more akin to resignation and a tinge of ironic amusement.

"I will protect you Jim…from now on you are mine."

"Only if you are also mine Khan…you realize officially you're known as John Harrison right? There is no way I can call you that unless in an official setting though."

Jim was nervous so he was rambling, he always rambled when he got nervous. Only this time he was cut off by Khan's soft lips pressing against his own. A muffled whimper came from Jim as he started to kiss back, making Khan reward him with a pleased purring sound. Jim pulled back, panting heavily as he looked up at Khan, a slightly dazed look on his face.

"Why…you…I don't…"

Khan placed one long finger over Jim's lips to silence him.

"Hush now…You know I will not harm you Jim."

"I know…but…I'm confused. Why would…someone like you…have any interest in me?"

Khan's gaze softened and he pulled Jim into his arms, smiling softly when the younger male curled into him like a cat seeking warmth.

"I had an interest from the moment I saw you trying to take on a group of angry Klingons by yourself Jim. Not many would be so bold, let along be able to hold their own for so long on sheer stubborn willpower."

Jim snorted in amusement and fell back onto the bed.

"Stubborn runs in my family Khan. It's a Kirk family trait."

Khan gave Jim a raised eyebrow and placed one hand over Jim's as Spock came into the room. Jim laughed at the obvious look of shock that passed over Spock's face.

"Relax Spock…he's been released. We're going to take him to New Vulcan to see some mind healers though…and there are other conditions too."

"One of which is that I am to remain by Jim's side from now on and assist him with anything he asks of me…not that I require orders to have that desire."

Jim blushed a bit and cleared his throat as Spock looked at him again.

"Everything's going to be fine now Spock…no worries right? Is Scotty still mad at me?"

"Negative Captain. Mr. Scott would like to convey his upset at you giving your life to save the ship, but he holds no ill will towards you."

Jim let his head rest on Khan's thigh and failed to stifle the snickering that burst forth.

"You can't just give a simple yes or no can you Spock?"

"Affirmative."

Jim burst into another fit of giggles and glared at the bag of pain meds he was hooked to.

"This stuff makes me act funny…I hate hospitals."

Khan gave Jim a fond look as he whined softly about his current state and location. He ran his long fingers through Jim's hair, smiling gently as he felt the younger man relax and drift into much needed sleep.

"Sleep well…my Captain."

Spock watched the exchange and saw the bond between them as most others would not be able to, heard the love in Khan's voice…something he hadn't thought possible with the super human. He backed out of the room and nearly gave a small smile of his own. His friend and Captain had gained a powerful protector, and it made him worry just a bit less for the reckless man's safety.


End file.
